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Series GSE79838 Query DataSets for GSE79838
Status Public on Apr 01, 2018
Title Methylome analysis of colorectal cancer cell line DNA (HCT116) and colorectal cancer patient derived xenografts (PDXs) using MeDIP-seq and cfMeDIP-seq
Organisms Homo sapiens; Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Three separate experiments were carried out using MeDIP-seq and cfMeDIP-seq for methylome analysis. For the first experiment, different starting amounts of HCT116 cell line DNA, sheared to mimic cell-free DNA, were analyzed using MeDIP-seq and cfMeDIP-seq. In the second experiment the limit of detection of cfMeDIP-seq was tested using varying dilutions of colorectal cancer cell line DNA (HCT116) with multiple myeloma cell line DNA (MM1.S). For both cell line DNA samples, the DNA was sheared to mimic cell-free DNA. In the final experiment, we tested the enrichment of human ctDNA using cfMeDIP-seq performed on plasma collected from patient-derived xenografts (PDXs) generated in mice from two colorectal cancer patients.
Overall design The gold standard MeDIP-seq protocol using 100 ng of sheared cell line DNA and the cfMeDIP-seq protocol using 10 ng, 5 ng, and 1 ng of the same sheared cell line DNA was performed with two biological replicates. For the samples starting with less than 100 ng of DNA, as part of cfMeDIP-seq, the DNA starting amount prior to MeDIP was inflated to 100 ng using filler DNA in the form of unmethylated and artificially methylated PCR amplicons. For the second experiment, using HCT116 and MM1.S cell line DNA sheared to mimic cell-free DNA, a serial dilution was performed using a starting DNA amount of 60 ng with HCT116 DNA diluted with MM1.S DNA. The varying percentages of HCT116:MM1.S DNA included: 100% HCT116, 10% HCT116, 1% HCT116, 0.1% HCT116, 0.01% HCT116, 0.001% HCT116 and 100% MM1.S. These samples were subjected to cfMEDIP-seq, with the DNA starting amounts prior to MeDIP inflated to 100 ng using filler DNA as previously mentioned. In both experiment 1 and 2, the sequenced reads were aligned to reference genome hg19. For the PDX-driven experiment, cfMeDIP-seq was performed on two plasma samples from mice engrafted with colorectal cancer patients-derived xenograft (PDXs). In this experiment, both the cfMeDIP-seq samples and their respective input controls were sequenced. The sequencing reads were aligned to both reference genome hg19, and reference genome mm9.

The PDX samples (GSM2422520 - GSM2422527) have no associated processed data. Conclusions for these samples were based solely on alignments. Raw data for these samples are represented by BAM files.
Contributor(s) De Carvalho DD, Singhania R, Shen SY
Citation(s) 30429608
Submission date Apr 01, 2016
Last update date May 15, 2019
Contact name Daniel De Carvalho
Organization name Princess Margaret Cancer Centre
Street address 101 College St
City Toronto
State/province ON
ZIP/Postal code M5G 1L7
Country Canada
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (24)
GSM2104457 100ng rep1
GSM2104458 100ng rep2
GSM2104459 10ng rep1
BioProject PRJNA317165
SRA SRP072765

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE79838_RAW.tar 112.9 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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